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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: Perl.t,v 1.7 2003/10/25 14:52:22 heikki Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS $DEBUG $BIODBTESTS);
$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
my $error;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
$error = 0;
if( $@ ) {
use lib 't';
}
use Test;
$NUMTESTS = 14;
$BIODBTESTS = 5;
plan tests => $NUMTESTS;
eval { require IO::String };
if( $@ ) {
print STDERR "IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping some tests.\n";
for( 1..$BIODBTESTS ) {
skip("IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping some tests",1);
}
$error = 1;
}
}
END {
# clean up after oneself
unlink ( 'Perltmp' );
for ( $Test::ntest..$NUMTESTS ) {
skip("Unable to run db access tests - probably no network connection.",1);
}
}
use Bio::Perl;
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run.
my ($seq_object,$filename,@seq_object_array);
# will guess file format from extension
$filename = 't/data/cysprot1.fa';
ok ($seq_object = read_sequence($filename));
# forces genbank format
$filename = 't/data/AF165282.gb';
ok ($seq_object = read_sequence($filename,'genbank'));
# reads an array of sequences
$filename = 't/data/amino.fa';
ok (@seq_object_array = read_all_sequences($filename,'fasta'), 2);
$filename = 'Perltmp';
ok write_sequence(">$filename",'genbank',$seq_object);
ok ($seq_object = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA","myname","AL12232"));
my $trans;
ok ($trans = translate($seq_object));
ok ($trans = translate("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA"));
ok ($trans = translate_as_string($seq_object));
ok ($trans = translate_as_string("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA"));
# we need to keep tests that depend on net connection at the end
unless ( $error ) {
# swissprot
eval {
ok ($seq_object = get_sequence('swissprot',"ROA1_HUMAN"));
};
if ($@) {
if($DEBUG) {
warn "Warning: Couldn't connect to SWISS-PROT! Do you have network access?\n";
}
exit 0;
}
# embl
eval {
ok ($seq_object = get_sequence('embl',"BUM"));
};
if ($@) {
if($DEBUG ) {
warn "Warning: Couldn't connect to EMBL! Do you have network access?\n";
}
exit 0;
}
# genbank
eval {
ok ($seq_object = get_sequence('genbank',"AI129902"));
};
if ($@) {
if($DEBUG) {
warn "Warning: Couldn't connect to GenBank! Do you have network access?\n";
}
exit 0;
}
# refseq
eval {
ok ($seq_object = get_sequence('genbank',"NM_006732"));
};
if ($@) {
if( $DEBUG ) {
warn "Warning: Couldn't connect to RefSeq! Do you have network access?\n";
}
exit 0;
}
# genbank
eval {
ok ($seq_object = get_sequence('genpept',"AAC06201"));
};
if ($@) {
if($DEBUG) {
warn "Warning: Couldn't connect to GenPept! Do you have network access?\n";
}
exit 0;
}
}
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